Related papers: Speciation due to hybrid necrosis in plant-pathoge…
The relationship between microscopic observations and macroscopic behavior is a fundamental open question in biophysical systems. Here, we develop a unified approach that---in contrast with existing methods---predicts cell type from…
We consider self-tolerance and its failure -autoimmunity- in a minimal mathematical model of the idiotypic network. A node in the network represents a clone of B-lymphocytes and its antibodies of the same idiotype which is encoded by a…
Protein-protein interactions drive many biological processes, including the detection of phytopathogens by plants' R-Proteins and cell surface receptors. Many machine learning studies have attempted to predict protein-protein interactions…
We study numerically how the structures of distinct networks influence the epidemic dynamics in contact process. We first find that the variability difference between homogeneous and heterogeneous networks is very narrow, although the…
The vertebrate adaptive immune system provides a flexible and diverse set of molecules to neutralize pathogens. Yet, viruses such as HIV can cause chronic infections by evolving as quickly as the adaptive immune system, forming an…
We introduce a model for multi-agent interaction problems to understand how a heterogeneous team of agents should organize its resources to tackle a heterogeneous team of attackers. This model is inspired by how the human immune system…
Current theories about mechanisms promoting species co-existence in diverse communities assume that species only interact ecologically. Species are treated as discrete evolutionary entities, even though abundant empirical evidence indicates…
Proteins need to selectively interact with specific targets among a multitude of similar molecules in the cell. But despite a firm physical understanding of binding interactions, we lack a general theory of how proteins evolve high…
Genomic duplication-divergence events, which are the primary source of new protein functions, occur stochastically at a wide range of genomic scales, from single gene to whole genome duplications. Clearly, this fundamental evolutionary…
During bouts of evolutionary diversification, such as adaptive radiations, the emerging species cluster around different locations in phenotype space, How such multimodal patterns in phenotype space can emerge from a single ancestral…
The striking variety of macroscopic morphologies displayed by bacterial colonies depends on microscopic environmental and behavioural details in a manner that is currently not well understood. A surprising example is sibling inhibition,…
During contagion phenomena, individuals perceiving a risk of infection commonly adapt their behavior and reduce their exposure. The effects of such adaptive mechanisms have been studied for processes in which pairwise interactions drive…
One strategy for winning a coevolutionary struggle is to evolve rapidly. Most of the literature on host-pathogen coevolution focuses on this phenomenon, and looks for consequent evidence of coevolutionary arms races. An alternative…
Species richness varies widely across the tree of life, and there is great interest in identifying ecological, geographic, and other factors that affect rates of species proliferation. Recent methods for explicitly modeling the…
Genetic diseases can be classified according to their modes of inheritance and their underlying molecular mechanisms. Autosomal dominant disorders often result from DNA variants that cause loss-of-function, gain-of-function, or…
Maintaining genetic diversity as a means to avoid premature convergence is critical in Genetic Programming. Several approaches have been proposed to achieve this, with some focusing on the mating phase from coupling dissimilar solutions to…
We present an individual-based model for two interacting populations diffusing on lattices in which a strong natural selection develops spontaneously. The models combine traditional local predator-prey dynamics with random walks.…
Generative adversarial networks (GANs) are pairs of artificial neural networks that are trained one against each other. The outputs from a generator are mixed with the real-world inputs to the discriminator and both networks are trained…
Uncontrolled, excessive production of pro-inflammatory mediators from immune cells and traumatized tissues can cause systemic inflammatory issues like sepsis, one of the ten leading causes of death in the United States and one of the three…
The self-protection of alliances against external invaders is a key concept behind the maintenance of biodiversity in the face of natural selection. But since these alliances, which can be formed by different numbers of competitors, can…